


A Second Shot at Life

by justanotherfangirlwriting



Category: The Shadowhunter Chronicles - All Media Types, The Shadowhunter Chronicles - Cassandra Clare
Genre: F/M, Family, Gen, Jonathan's life after CoHF, M/M, OC behaviour, Second Chances, i still don't know how to tag
Language: English
Status: In-Progress
Published: 2016-12-31
Updated: 2018-04-06
Packaged: 2018-09-13 14:22:14
Rating: General Audiences
Warnings: Creator Chose Not To Use Archive Warnings, Graphic Depictions Of Violence
Chapters: 9
Words: 14,989
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/9127579
Author URL: https://archiveofourown.org/users/justanotherfangirlwriting/pseuds/justanotherfangirlwriting
Summary: My name is Jonathan Christopher Morgenstern. For all my life I lived in suffering and pain as demon blood filled my veins. I have killed more people than I can count. I had a father but he is dead. I have a mother, but she does not know that I am live. I have a sister I doubt she will ever forgive me. I have been given a second shot at a life that I did not get to live. No one knows that the demon boy is alive, but I am no longer a demon boy. I am nephilim, but can never return to the shadow world. Or so I thought.





	1. Chapter 1

**Author's Note:**

> This story is un beta'd so be warn there maybe some mistakes. 
> 
> The first few chapters set out Jonathan life after the events of CoHF, this is in the TMI world but it will be treated as an OC story.

**2016 - 9 years since the dark war - London.**

Jon wakes from his nightmare. The same nightmare that plague his nights. Most nights he draws a dreamless rune on him, but sometimes he forgets. The dream is of death, destruction, and his mother's tearful face as he looked up at her, wanting to apologise for everything that he had done, for the pain he's had caused her. But he was jolted awake when his phone rings. Jon groans and tossed his pillow at it. It stopped, then it ran again, he sighed and picked it up. It was a message from his friend.

_**Kendra: You better not be asleep still! I swear Jon you are always late which makes me always late because you're my ride. Get up!!!** _

_**Jon: I'm awake. Now. Honestly Kendra you can take the tube to work like a normal person if you don't want to be late.** _

_**Kendra: The tube is filled with perverts last time I took it some bloke felt me up. -_-** _

Jon smiled. Kendra was the first real friend he had made in his whole life. He ran into her, literally, the first day he arrived in London. She screamed at him because he had accidentally spilt her drink on her new dress.

Deciding not to piss her off more, he got up from the bed. The whole apartment, minus the bathroom, was a wide open space. Tall windows let in the morning light, he stretched and did a few sit ups then headed for the bathroom. Jon didn't sleep in the bedroom because it made him claustrophobic. And reminded him of a life that he lived for so long. So he made the bedroom into a home work space ad dragged the mattress into the main room.

As Jon looks into the mirror and he doesn't see the body of normal 25, soon to be 26, year old man. He sees the body of a warrior. Who has seen and done so many horrible things. He traces the runes on his arms, his chest, and the stab wound where everything, the pain, the sorrow, disappeared. Some days he thinks he's just dreaming, which he never did when he was him. he goes into the drawer and pick up the only thing he brought from his past, his stele, only used to draw a glamour, or voyance, rune to hide all the scars and runes from his body.

Jon then gets into the shower then changed into some clothes, black jeans, a button up shirt with black and white stripes. Jon works at a publishing house where he edit books and manuscripts. He has always enjoyed literature, mainly he read books on war, but after he came back Jon started to read other books, classic mundane literature and read them all. Jon was thankful of finding Kendra since she worked at a publishing house, she was an assistant and he was 18 when I met her, she was 19. He had no identification, no proof of life on him, then he remembered his father's loft, one of many he would use when we would travel, there was a glamour charm on it so only they knew where it was. He had papers in there just in case he would need it. She helped enrol Jonathan into university, she recommended him to the place where she worked and he's have been there ever since. 9 years since everything. He's built a life in London, made friends, with the people he use to think inferior. He left his flat and made his way to his car to go pick up Kendra.

The shadow world is all over. Especially in big cities like London. Over the years he has had close encounters with it. At a club where most of the faeries tend to hang out, at the park, in the city. Jon knows can't escape them, but he's learned to avoid them. But he does miss it, of course, it's his world and what he wanted to be. He wanted to be the best Shadowhunter. Fighting demons, instead he was one, or at least half.

The drive from his place to Kendra's was about 15 minutes she lived in Camden, where as Jon's flat was in central London. Valentine always liked being in the centre of it all. Once he arrived he texted her telling her he was downstairs

_**Jon: how is it that you message me to get ready, when you yourself aren't even ready.** _

_**Kendra: haha. I am ready I just decided to change my clothes. Be down in 5.** _

As Jon waits for Kendra, he looked around, to the mundane eyes, people were just waking up and getting ready to start there days. To his eyes, there were downworlders all around doing the same. A family of werewolves walking down the street, 2 faeries having tea in what he knows was a faerie ran cafe. Vampires were never out in the morning but they're here somewhere.

Jon's spying was interrupted when his car door slammed. He turned and look at Kendra who was fuming.

"Fighting with Sam again?"

"Don't even get me started. She's unbelievable."

Sam was Kendra's sister who recently moved in with her from finishing university up in Wales.

Kendra was of mixed heritage, her family is Welsh but her mother's family came from Japan. Kendra was beautiful to the untrained eye but when you look at her she's beyond. Her dark hair was short in a shoulder length bob, hazel eyes that were hardly seen in Asian eyes, she was short but you don't even notice it because if the way she holds herself. All bite and no bark. She rants all the way to the office. Even when they exited the car she still talks like it was just the two of them the car, she doesn't care if people look at her.

"Kendra calm down, you're turning red." Jon laughed. They stood in the lift silently, she was trying to calm down, the runes maybe hidden but they were still activated, he can hear her trying to calm her breathing.

They arrived in the office, Jon was the youngest editor they had on staff so he had his own office and an assistant.

"Hey Michael anyone called?"

"Yeah, a message from head office saying they need to see you as soon as you came in."

Jon nodded and placed his bag on the table. He said goodbye to Kendra who sat on her desk. Head office was a floor above us so Jon took the private lift that lead straight into them. He greeted the people who worked there and knocked on the door. His boss, Genevieve Corsett was the youngest and most feared CEO of the publishing world, she's only 32 and she runs a worldwide publishing company. When Jon entered she was on the phone, she notice him and motioned for him to sit. While Gen may scare most people she didn't scare Jon. And that's why she likes him. He doesn't cower when she speaks.

"Okay I'll be there in a few days. Just don't do anything big. Just finish planning the launch." She hung up the phone and told her assistant to close the door.

"stressful launch?" he asked, Genevieve's Publishing House, Corsette House was always, or it seems, opening new branches in different cities. She's opened 8 alone this year or at least expanded.

"You have no idea." She rubs her temple as she sits on the couch.

"So what did you need me for?"

She looked at the door, Jon got up and sat next to her.

"Okay so you know about the new Publishing Launch in New York this week?"

Oh no.

"Well something went wrong with the books and the edits are all messed up. And the author wants the book to launch this week because of the holiday season. He can't be persuaded, David is doing everything he can but nothing can be done. You're our best editor so I was wondering if you would go to New York with me?"

Jon understood the pressure she was in, Genevieve had a lot on this book it was the company's best seller book.

"Gen you know about me and New York."

"Yes I know your family issues, but Jon I would not ask you if it wasn't important."

"Can I think about it?"

She sighed. But nodded. "I need your answer by the end of the day." Jon nodded and got up and left her office. Michael was waiting inside his office with new manuscripts.

"Ooh bad meeting?"

"No- Um it's nothing. Just stuff. Are these all I have to check?"

"Yeah. It's the holiday season, so people decide to send in a lot of manuscripts for final checks." Michael set the pile down on my desk.

Jon sat down and went on his personal computer. Shadowhunters were pretty anti technology, although he's pretty much caught up and he knew Clary was raised as a mundane so he manage to check up on her. From an outsiders point of view she was a normal 25 year old. It looks like she and her friend Simon were Parabatai, Jon saw the rune on her collarbone and his arm. His mother was married to her werewolf friend Luke or Lucien. Valentine always said if Shadowhunters were turned into wolves or vampires that they should stop living because it's dishonourable. But Jon stopped believing in that. Social media was one way to keep track of his family, even if they didn't know it.

For the rest of the morning Jon was on autopilot. Reading the papers on his desk, correcting the mistakes, thinking about Gen's offer, actually considering it. By noon Kendra knocked on his door.

"hey you ready-"

"Woah what's up with you?" She asked. When she saw Jon. He knew he looked like hell.

"Close the door." She did as she was told and sat on the chair in front of his desk.

"Gen's asked me to go to New York with her. She needs help with a difficult author."

Kendra, like Gen, knows about Jon's issues with his family, they don't know the full story, no one in Jon's new life did, but she knew enough. How he did something that was unforgivable to his family. And why He left and never looked back.

"Listen Jon it's been 9 years. Don't you think they would have forgiven you already?"

"You don't know what I did Ken. It's not something easy to forget."

"You never know Jon. Besides this is a big deal for the house. It's important." With that she left him with his work and thoughts.


	2. Chapter 2

**Notes for the Chapter:**

> This story is un beta'd so be warn there maybe some mistakes.
> 
> The first few chapters set out Jonathan life after the events of CoHF, this is in the TMI world but it will be treated as an OC story.

After work Jon decided to go to the dojo where he trained. He goes there 3 times a week to train and let his muscles work. If Jon couldn't put his training in the field he might as well do it in martial arts. They were moves that Jon was trained with all his life. He was familiar with because he's trained in jujitsu, karate, Krav Maga, and a lot more.

After he burned out his energy Jon headed straight home. As he approached the door he heard music playing, Jon stopped, no one knew where his flat was, aside from those he was close with but no one told him they were coming over, and no one had keys. He didn't have weapons with him, he never does, they're always hidden in the flat.

Jon opened the door slightly, He activated the silencing rune on my hip. Jon turned the corner ready to attack, but relaxed when he saw it was Gen.

"Gen you scared me. What are you doing here? And how'd you get in?

"What a woman can't visit her boyfriend anymore? Also you left these at on my couch." She held up his keys, he didn't even realised he dropped them.

Jonathan has been with Gen for 3 years now, very few people knew because she was his boss and for someone his age to hold a high position in the company and be dating the boss people tend to talk. Jonathan never really cared about what people thought, but Genevieve did so he agreed to a quiet relationship. When they first met it was his first year as an actually editor. She wasn't the CEO yet, it was her father, but he was grooming her to take over. She always had a sense of leadership even then. That was the reason why he was drawn to her, and why she was drawn to him, since Jonathan didn't find her intimidating she instantly enjoyed his company. It took him a few years to ask her out to dinner but once he did she said yes, that was the first time Jonathan saw his life actually become even more normal.

Jon smiled and relaxed. He went up to her and kissed her. She smiled into the kiss and pulled him towards her. Jon pulled away and stroke her cheek, he placed a kiss on her forehead.

"Of course you can. Sorry about that." He said

"Yeah you seemed pretty jumpy. Are you okay?"

"Yeah I'm fine I just got back from the dojo. I guess the adrenaline is still pumping."

She seemed to believe the answer, which was true, and dropped the topic.

"Smells good. What are you cooking?" He wrapped his arm around her and placed his chin on her shoulder.

"Curry. Felt like it."

"Okay well I'm going to shower." Jon said as he left her to finish her master piece, cooking always helped her relax, just as training helped him. There was a training room in the flat, but he preferred training with others.

Jon went into the bathroom and stripped from his gym clothes. He took a quick shower. The glamour he drew was faded so he had to apply it again. While Genevieve doesn't have the sight she can see the scars on him and he did not want to explain where they came from. After placing the new glamour on the old one, he headed for the main room. She already set up the plate and food in front of the tv. Jon sat next to her and started to eat. She was watching him, she clearly had another reason of coming over. She wanted his answer. Jonathan purposely avoided her after work since he did not have her answer.

She placed her hand on the nape of his neck. "Jon I know you don't want to be in New York and I swear if I had another choice I would take it. But I don't."

Jon placed his fork down and stopped eating, he looked at her.

"New York is a place I said I would never step foot in again. But it doesn't look like I have a choice. This is important to you and to the company."

She smiled and kissed him.

"I swear we'll be back in London before you know it."

She smiled. He hope she was right and he hope the trip to America would be smooth but with his life, he knows karma is going to bite him in the ass.


	3. Chapter 3

**Notes for the Chapter:**

> They're in NYC finally! The story will pick up as it goes. Remember this a is completely OC work with touches of the book. But everything in it is OC

They arrived in New York around 9 am on Thursday. The Launch was on Saturday so they had 3 days, counting Thursday, to fix what went wrong during the launch set up. They didn't have time to change. They sent their stuff up to the room and headed to the New York Branch of Corsett Publishing.

The morning was hectic. Jon was not feeling well ever since he landed in the city. Maybe it was air sickness but he knew it wasn't normal. Jon just kept looking over his shoulder worrying if he would catch some downworlders or nephilim. So far no one. Jon kept his stele in his pocket, he also kept a dagger tucked into his a ankle hostler. After the meeting Gen decided she was hunger, and if he were to be honest he was too,

"So where do you suggest we eat?"

Jon shrugged, "honestly Gen you have a better understanding of the city than me. It's been years since I've been here."

"Yeah but I want to know if you have a favourite spot in the city."

"Not really. New York isn't even really my home. It's my mother's and sisters. But I grew up-- traveling with my father."

"Hmm. Okay well come on I know the perfect place." She took his hand and headed out.

\--

Middle of the day in New York. Mundane go about their lives as if nothing is happening. Clary use to be like that, she missed it. It's been years since she found out who she really was but she always finds herself between worlds. She was raised a mundane so she knew what they were like. She kept up with her social media and she kept up with her mundane friends. But she was also a shadowhunter a leader of the NY Institute, one of the youngest, at 25, she has proven herself in more ways the one. Right now she was patrolling the Upper West Side, Magnus said there were some rogue downworlders, probably the Fae, causing issues with the factions of wolves in the area.

She was looking at the Faerie cafe when she notice something in the corner of her eye. She activated her farsighted rune.

No. Not possibly, it can't be. It was Sebastian, but it can't be he's dead, she saw him die. His body left to be buried. But it was him, but he was different. He was smiling, a genuine smile. And he was with someone, a women, who happens to be mundane. Clary would have thought her eyes were playing games with her but the man turned and she saw it. The Morgenstern ring, the same ring she wore around her neck. Was also around his. Clary nearly fainted.

But here rune made everything clear. His eyes. Oh his eyes, they weren't the cold dark black color she was use to. They were the green of her eyes. The green of what her brothers eyes should have been.

Clary snapped out of it and portal away. She needed to get to the bottom of it.

\--

There was that feeling again, like he was being watched. He and Gen were stood by a hot dog cart of all places, she said they have the best hot dogs in the city. She said something that made him chuckle but he was only half paying attention.

"Hey Gen can I meet you back at the hotel. I think I left my phone back at the office."

"I can go with you."

"No it's okay. It's getting late and we haven't slept for almost 20 hours."

Jon kissed her goodbye and headed back to the office. Once Jon knew he was away from her view. He turned into an alley and hopped onto the roof, his agility was always better than any nephilim, even with the demon blood burnt out, Jonathan trained more than anyone, maybe not Jace, but their father trained them the same but tougher on Jonathan. He surveyed the streets but saw no one out of the ordinary. Just normal mundanes and occasional downworlders living their lives.

"What are you doing in town Jonathan?" Jon jumped at the voice behind me.

It was Brother Zachariah or Jem Carstairs.

**_9 Years Ago - Idris Crypt._ **

Jonathan takes his first breath in hours. He looks around and sees he in a dark room, no he's in a crypt. He looks down, he was wearing the clothes he died in, the sword where his sister stabbed him and burnt out the demon blood and was suppose to be his end. He got up and nearly fell, he's never felt so light, so free from the blood that burned him all his life. His first thought was 'I'm alive.' Then it came back to him. Everything he had done, or Sebastian as done. All the lives he had taken and destroyed. If he revealed himself alive, the nephilim would have him killed before he could say anything to defend himself. He couldn't go back. No.

Jonathan didn't realise someone was with him. He looked at the person, it was a man. Late teens or early 20s. He had dark hair, with a white streak on it.

"Who are you?" Jon asked. For the first time in his life afraid.

"I was brother Zachariah. But you can call me Zachariah, for now."

"What do you mean was?"

"Well like you Jonathan I too was cursed. For many years, I lost everyone I loved, well minus one, I lost my Parabatai, my friends, but the heavenly fire gave me a second chance. And I think that's what it did for you. Giving you the life you didn't have before."

"Does that mean I can go back to my family?"

"No. Sebastian has ruined a lot of people's life and they may not be forgiven I suggest you live your life outside the nephilim."

"But how? I'm still nephilim. I'm a warrior. We were born for the fight."

"It won't be easy Jonathan. But you can do it. If you need me just say this spell. I know a warlock and she'll help. I must go. She's opened a portal outside. It will take you where ever in the world. Good luck Jonathan."

With that he was alone because Zachariah left the room. He left him some clothes. That was the last time he saw the ex silent brother. Until now.

\--

"Why are you here Jonathan?"

"Did you put a tracker on me or something?" Jon wondered how he had found out that he was in the city.

"No. But my wife has been keeping an eye on you since our last encounter."

"That was almost 10 years ago. And if you must know I'm in the city because of my job."

Jem looked at him, like he was trying to make sure that he wouldn't cause any issues.

"It's been years since you've set foot in this city. A lot has changed, especially in the shadow world. Be careful Jonathan and do not get caught. If the Enclave finds out you are alive, it would not be good."

In the blink of an eye Jem drew a rune in the air and a portal appeared, one of Clarissa's creations he believes. His sister was a special case, being able to create new runes.

"Be careful Jonathan" and with that Jem stepped into the portal.

 

Deciding that using the portal rune would have been dangerous since he knew the clave uses a tracking rune for all the rune activities in the city, Jon thought it would be safer just to take a cab. He looked around making sure no one was passing the alley before he jumped down.

He was hailing a taxi when someone knocked him out then everything was black. 


	4. Attention:

**I will be moving this story to my Wattpad account (marielleswriting) but I will still update it on here, it may be slower because I'm focusing it on Wattpad but I will try to update it here as well.**


	5. Chapter 4:

**Notes for the Chapter:**

> This story is un-beta so be warned there may be some mistakes.
> 
> This is in the TMI world but it will be treated as an OC story.

When Jon woke up he was alone in a small room, with only the chair he was sitting on and a mirror as furniture. He tried breaking free from the ropes that were tying his hands but there seemed to be a rune on it. "Crap." He was grabbed by some Nephilim.

"Damn." He cursed. Jon stopped struggling when he saw the door open, getting ready to attack but he also felt that his foot was tied as well, they really went at it with the restraints, not that he could blame them. He kept his face blank but he was panicking inside. He can't believe they found him.

"How are you alive?" The man said, a seraph blade in his hand, he was in his early 30s, brown hair, in a ponytail that showed an agility rune on his neck. Jon didn't say anything, he just looked at him, his eyes may not be black anymore, but his gaze was still frighten, all those years of scary people and killing them, came rushing back and he hated it, he looked away.

The man chuckled,

"Sebastian Morgenstern, in the flesh—," once that name was said Jon glared at the man and said his first words since he saw the man.

"That's not my name."

The man jumped back at the tone of Jonathan's voice, but then he composed himself and said.

"So what should I call you then?"

"Jonathan." The man straighten up and left the room with no other words. Jon looked at the door, and if his eyes weren't playing tricks on him, he could have swore he saw a glimpse of red hair.

—

"Well?" Clary asked, looking at Artem, who was their best interrogator since he could easily spot a liar just by talking at them.

"He didn't give me much to get a read on him, but that anger he showed when I called him Sebastian, that was real and honest."

Jace held Clary hands, he didn't believe her at first when she portal into their office and said that she saw Sebastian, but when she showed him what she saw he was shocked. They saw him die, saw him being taken away from Jocelyn's weeping form. But the man in front of them was clearly him, but it also wasn't. Even without Artem's special talents, he knew Seb- Jonathan wasn't lying, as much as Jace didn't like to admit it, he knew him. Being bonded to a person, even by force, does that to you. It wasn't like the way it was with Alec, with Jonathan it was a weaker bond after the heavenly fire separated them but he could still feel it, when Jonathan died, it dulled. Then a few hours after he felt it but ignored it because knew, or thought, Sebastian was gone.

Artem looked at them, "Didn't you say that when he died, Jonathan appeared in him? Maybe that's what this is?"

Clary has considered this, when she saw those eyes, it was like she was back in the Edom again, watching her mother hold her brother's dying body as she cried and held on to a child she would never know. Those green eyes, that mimicked her's and her mother's eyes.

She looked at the window, the man was just starring at the mirror as if he knew they was out here.

"Clary what do you want to do?" Jace asked, his eyes not leaving the window

"Get him talking. Ask him what he is doing here." Clary didn't know what to believe but with him showing up after all these years, and the Seelie Queen seems to be planning something, it could all be connected.

Artem nodded, and went back into the room.

—

"So, Jonathan. What are you doing here in New York."

"Why does it matter? Whatever I say you won't believe it? So why not save my breath?"

"Try me, I'm a very understanding person." Artem said, his eyes never leaving Jon's, Jon knew Artem was trying to see if he was telling the truth or not, some Nephilim are born interrogators, they could always tell when someone was lying. But Jon wasn't, he hasn't told a lie since he started talking to Artem.

"I came here as a favor to a friend. For work."

"You have a job?"

"Yeah it's been 9 years, how did you think I survived?" Jon said, the snark rolling off his tongue. He didn't care if they didn't believe him. All he wanted was too leave and forget this encounter but he knew he wouldn't be able to forget.

"Well Jonathan, I hope you wouldn't mind answering some questions." Artem said, leaning on the mirror.

"Do I have a choice?" Jon sighed.

Artem smiled, "No I guess you don't."


	6. Chapter 5:

**Notes for the Chapter:**

> This story is un beta'd so be warned there may be some mistakes. this is in the TMI world but it will be treated as an OC story.
> 
> This is also up on Wattpad my username over there is marielleswriting. That is where I will mainly keep this story up to date.

Clary played with the Morgenstern ring around her neck, she watched Artem asked, she couldn't even say the name without a lump forming in her throat. She noticed Jace left her side, she turned around and saw that he was on his phone, he gave her a supporting smile. She tried to match it but she couldn't, she turned her head back to the window, she can tell her brother was getting irritated. And the phone in his jacket they took from him kept on ringing nonstop. She didn't have to look to know it was someone named Gen calling him, she's been ringing his phone and texting for the last hour. She must really care for him, his wallpaper was of him and the girl, so she must have been his girlfriend. Clary has been reasoning with herself since Jonathan came in, if someone cared this much for him, he couldn't be the same person right?

  
Jace came back and looked at the window as well. The room was sound proof but the look in Sebastian's eyes, he will call him Sebastian until they know for sure. But even he's doubting that this is the same guy who killed all those people. But whatever he or Clary thought, it wouldn't help. This is still the face and body, who murdered so many of their people. If the clave ever found out about him, they wouldn't think they would just kill him, for real.

"That was Raj. He said Jocelyn's tried losing him twist already. She's probably making her way here."

Clary looked at Jace here green eyes looking frantic, "She can't see him, Jace. She's already mourned him, twist, she can't see him. Until we know for sure."

Jace didn't notice how upset Clary was until she wrapped her arms around herself. Clary's changed in the past decade, she was a warrior now. She was like Isabelle, but even in small moments, she was still a girl who is looking at the brother she thought she would never meet. But she is also looking at the brother she hated. The brother that caused so many problems for the both of them.

  
Jace wrapped his arms around her, Clary relaxed at his touched. Artem signaled them that he was done, and coming out.

Artem came out, he didn't look any different but his shoulders looked more relax than when he started with Sebastian.

"Well?" Jace asked,

"He's not lying. He told me a lot of things, though he's holding back. He works at a publishing house in London, he's in New York for an opening. And he really hates being here. He hasn't said anything, but I can tell he senses you two, every time I mention any of you, he stiffens and doesn't answer me."

Before they could ask Artem anything else the door opened, Jocelyn Fairchild looking like she ran all the way here from Brooklyn was standing in front of them looking at them, then at the window that clearly shows her, not so, dead son. Jace glared at Raj who followed Jocelyn in,

"what the hell happened to keep her away from the Institute?!" Jace asked.

"She evaded me, I had to chase her up and down the village then she portaled here." With a groan Raj left them alone, ugh if he wasn't such a good Shadowhunter Jace would have probably kicked him out.

"Mom," Clary said, her voice was small, trying to stop her mother from doing anything that would be considered dangerous, like barged into the room where Sebastian was. But Jocelyn didn't look at them, she was just looking at Sebastian who was staring at the mirror, straight into their eyes.

"Is he—?" Jocelyn asked not looking away from her son. She can't do this again, she buried him, she accepted that he was gone, that he never existed. That a demon child took the place of a son she would never know, but here he was now, sitting in front of her. His green eyes mirroring her own eyes and Clary's. The white blond hair was replaced by an ashy blonde, that matched Valentine's hair before all the demon experiments turned his own hair white.

"He's what he says he is. It seems like he knows what he has done so it's not a trick. He hasn't shown any intention to lie. But that's all we know."

"Mom, listen you don't have to be here. We can-,"

But Jocelyn wasn't listening, she headed for the door and opened, then shut it. She placed a rune on it so it wouldn't be opened from the outside. She turned around and she finally sees him. He looked surprised and was about to say something but didn't, he just looked at her. She slowly walked up to him, if he could move from the chair he would have probably backed away from her. Jon could hear the banging on the door, what was he going to do? Attack his own mother? His old self probably would, but now? All he wanted to do was hug her. She was the first person he has seen from his old life that he hurt. All he wanted to do was apologize to her, but he couldn't form any words. Jocelyn kneeled in front of him, she looked at him, trying to take in his face. Because he was here, he wasn't Sebastian, he was Jonathan. Someone she's pictured meeting all his life, from the moment he was born; wondering what he would look like with green eyes, how he would be with Clary, but that was all ripped away from her. She had tears in her eyes and hugged him, Jon didn't, and couldn't, do anything because he was tied up, he just relaxed into his mother's arm, burying his head into the crook of her shoulders, as she whispered his name over and over again.

The sight of her mother hugging the son she lost broke Clary in more pieces than one. They couldn't take Jonathan away now, they didn't even know what to do with him, all Clary knew for sure was that taking Jonathan away from their mother would do more damage than good. She didn't know if her mom could take losing him once more. They needed to tell the Clave, but first, they must prove that Jonathan wasn't who he was before. Because no matter what they do, he can never be fully accepted by the Nephilims. He's killed too many people.

Clary turned to Jace who was also looking at the mother and son, but unlike Clary, Jace kept a fully composed face.

"We have to call everyone in. Simon and Izzy should be back from recruitment by now. Alec and Magnus should be back from Idris."

"Why don't you do that? I'm more composed than you right now and I have to go in and talk to him."

"Jace-," Jace gave Clary a look,

"Clary please, I need to talk to him and see what we can do with him. Plus his phone has been ringing nonstop. Might as well give it to him and I don't think you're emotionally ready to see him yet, call Izzy and the others. Have them meet us in the office."

Clary knew Jace was right, she wasn't ready to face him, not yet. She kissed Jace and left the room. Jace looked back and saw that Jocelyn was now just talking to him. Jace took a deep breath and picked up Jonathan's jacket and stele. He could have easily undone Jocelyn's rune on the door but Clary told him not too. He drew the counteracting rune that Clary made a few years ago after a really bad mission. It counteracts any spells or runic magic. It was a life saver.

The door opened causing Jocelyn to stand in front of Jonathan. She relaxed a bit when she saw it was Jace but she still stood in front of him. She must have known Jonathan was capable of taking care of himself, even if he was tied up. But a mother's instinct, Jace guessed.

"Jace, what's wrong? What's happening?" Jace tossed Jocelyn the stele,

"Untie him." Jocelyn didn't ask questions, she just drew the counteracting rune, since the rune on the ropes that were binding Jonathan can only be undone by said rune. Once he was untied he flexed his wrist, Jace saw that he was wearing glamours, covering up his runes. Jonathan saw Jace looking,

"You can never be too careful, I live with mundanes, and you never know who might have the sight. Plus I have scars I would rather stay hidden from mundane eyes." Jon took his stele from his mother's hand and drew an iratze on his wrist for the rope burns.

"Your phone's been ringing nonstop," Jace said, tossing the cell to Jon.

"Can I call them back or am I still in jail?" Jon said, mildly annoyed at them for keeping him here for too long that Gen, he knew it was Gen, called him a thousand times.

"Oh you're still in jail but everyone gets one call. It's mandatory."

"Jace!" Jocelyn said, glaring at him.

"It's okay, I'm glad you're still the same Jace."

"I'm glad you're not. I think." Jace said all serious, he turned to Jocelyn,

"Clary needs your help, she up in the command center."

"Jace—," Jocelyn warned him, she didn't trust Jace alone with Jonathan, as composed Jace is, he wasn't Jonathan's biggest fan. Jocelyn didn't know what he would do.

"Relax, I'm not going to hurt him, I just need to talk to him. Plus I'm sure he can handle himself." Jace looked at Jonathan, who was dialing a number on the phone,

Jace knew that Jonathan was paying attention to the conversation he was having with Jocelyn, but he kept his eyes on the phone. Deciding not to argue Jocelyn left the two men in the room.

"Jonathan! Oh god, where the hell have you been? I've been calling you for hours now. I was getting worried. Are you okay?"

"Gen I'm okay. I ran into—," Jon didn't know what to say he had to tell her something, but he couldn't say the truth. So he decided to tell her a partial truth.

"I ran into my sister. I couldn't avoid her because she already saw me, so she asked me to talk. I guess I had my phone on silence. I'm sorry for worrying you. I'll be back at the hotel soon."

"Your sister? How did that go? Are you okay?"

"It went as expected. I'm fine, I'll tell you more about it later okay?"

"Okay, and Jon? I'm proud of you, I knew how hard it was for you to come back here, let alone talk to your family."

"Oh, you have no idea. But thanks, Gen, I'll see you soon."

Jace and Jonathan watched each other for a while, Jace didn't look any different from the last time Jonathan saw him. He was still the same golden boy that the Nephilim knew. His blond hair was shorter than the last time, his gold eyes were duller but maybe it was just the terrible lighting in this room. Jonathan knew that he looked different from the last time Jace saw him. He looked more healthy and not a ghostly pale like before. He was still pale, like Clary, but he had color in his face, he filled up a bit more, though he was still lanky. The biggest change was his eyes, they were no longer black, Jace couldn't look him in the eye for too long. Jon's hair was ashy blond and not pale white.

Jace didn't know what to make of the man in front of him. The way he held himself was different, Jace noticed, less high and mighty but nowhere near timid. The Morgenstern ring hung around his neck, like how Clary wears hers. She wears the Fairchild one on her finger like how Jace wears the Herondale ring he got from Tessa.

"Are you just going to stare at me or are you going to let me go? Look, Jonathan, I'm not a danger to anyone."

It was weird hearing Jon call Jace by their full name, since he was now going by the name and not Sebastian. He was the only one who called Jace, Jonathan. No one has called him that since the last time Jace saw him.

"Well sorry if we don't believe you." No matter how different he was, this man in front of him, or at least his face, was still the one who killed thousands of their kind, Jace wasn't an easily trusting person.

"I get that you don't trust me, monitor me, have Shadowhunters monitor my room. But I have to go."

Jace can see Jonathan getting upset but Jace saw Jonathan activate the Calm Anger rune on his neck. Jace knew that feeling, that feeling of wanting to scream and attack but Jonathan knew better than to react. He just took in his anger and looked at Jace.

"So what? I'll just stay here until you decide to completely ruin the life I've built."

Jace didn't give him a direct answer. "Get comfortable. I'll have some food brought to you soon. You can keep your phone and stele, but the opening rune won't work, Clary's very thorough when it comes to the runes she makes."

Jace then left Jon alone, at least he had his phone still. He really couldn't do much, he could have easily knocked Jace out and escaped but what would that show? Jon sighed, "This is going to be a long night." He said as he sat back down on the chair.


	7. Chapter 6:

**Notes for the Chapter:**

> This story is un beta'd so be warned there may be some mistakes. this is in the TMI world but it will be treated as an OC story. 
> 
> This story is also up on my Wattpad acct (marielleswriting) I will frequently update over there more. But I will also still be slow. I am currently still writing this story, as well as I'm still in college so I have work for that.

Clary called everyone to the institute but she didn't tell them what for, she didn't know how to explain it. So she waited for everyone to get back and for Jace to come up to the office. Her mom found her when she was heading up to, saying Jace said she needed her, it was probably Jace's way to get his alone time with Jonathan. He wasn't lying though when he said that Clary needed her mother. Because she did, once Jocelyn found her she took Clary into her arms, like what she did with Jonathan, and said that they will get through this together. Jonathan wasn't the problem here, all three of them knew it. What Artem was saying about how Jonathan wasn't lying was true, not matter what he does, no one can lie to Artem. Artem was half-fae and the only reason he escaped the cold peace was because he was a son of a high authority Clave member. But they put him to work of course and he has shown his loyalty. Their big problem was the Seelie Courts, they have been planning something and it was manifesting. They didn't know what it was, only that the Seelie Queen has sent out many of her knights to cause havoc in the Mundane world.

With Jonathan showing up it changes things. Once the queen realizes that Jonathan is alive, she'll stop at nothing to get him back. The Seelie Queen has always been a fan of Sebastian, who knows what she will do when she realizes that there is a version of Sebastian that is sort of untainted. Keeping Jonathan in the institute is for his safety and for theirs. But they needed to tell the Clave about what is going on. And once they do, it will not be pretty. When Jonathan was still knocked out she and Jace made a plan of telling the institute what was happening, but first, they needed to tell their friends and family. Clary was pacing in the middle of the room the door opened, she expected it to be Jace but it was Simon and Isabelle. She hugged them both, needing some comfort from them, she knew Simon could tell something was wrong because he hugged her tightly, he didn't ask but when he pulled away his eyes was scanning her face.

"So how was Texas?" Simon had a job from the Austin Institute, he was recruiting for them and Izzy went with Simon because she wanted to spend time with him, plus she could help some of the younger kids from the institute train, those who aren't old enough for the Academy.

"It was okay, we had some issues with the Faeries but not all of them believe in the Seelie Queen's cause."

Clary knew the Seelie Queen's rebellion was getting more prominent in the shadow world, but she didn't know that it was getting bad, Austin was a big city but it wasn't as big as New York or California was when it came to it's Shadow World.

"God Simon this is getting really intense, we will have to call in the Clave soon if this doesn't stop. I understood the Faeries were angry about the Cold Peace Treaty but this is getting out of hand. Just last night we had to take 4 Seelie knights into the City of Bones,"

"Alec and Magnus will be here soon, they'll tell us what dad knows," Izzy said. Alec and Magnus went to drop off Rafael and Max at the Lightwood Manor since New York was getting too dangerous, at least in Idris the Lightwood House is guarded with heavy wards.

"So why did you have us come over so quickly?" Simon asked as he greeted Jocelyn who was sitting on the couch.

"Let's just wait for Jace, Alec, and Magnus. Jace will explain once everyone gets's here."

A few minutes later Jace came in, with Alec and Magnus following behind him, even with all these faerie issues Magnus still manages to add glitter to everything, he was literally dripping in them as in as he walked in glitter fell from him. Clary smiled and greeted them,

"damn it Mags we just had the floor clean."

Magnus smiled at her, "sorry bout that biscuit," He waved his hand and the glitter disappeared from the floor. "there, all clean. So what's going on? Jace was quiet all the way up here, that's never a good sign." Magnus said.

Jace went by to greet Isabelle and Simon, "did you turn the monitor on?" Clary asked him.

Clary texted Jace to turn the camera on in the interrogation room, they normally had it off since they would normally stand on the other side of the window, but they needed to be as far from Jonathan, just in case Alec and Isabelle take the news badly. Jace nodded and Clary took a deep breath then turned the monitor on.

"okay, guys I want everyone to keep an open mind. And listen to the full story, we'll explain as much as we can."

Before anyone could reply the screen focused, for Alec and Isabelle it felt like the air was being sucked out of the room. They were looking at a man they both believed was dead, Sebastian, but he didn't look like himself, he looked older, he looked like what Clary would look like if she were blonde and a male. He looked more like Jace though, same blond hair, and built, though Sebastian was skinnier and had more of a lean look. His eyes though were all Clary and Jocelyn's.

"What the hell is this?" Alec asked, pushing off from the wall he was leaning on.

"I can explain," Clary said, standing in front of Alec, "earlier today I was monitoring the streets to see any weird demonic or faerie activities. Then I spotted something familiar, at first I thought the rune was playing games on me, but then I caught a better look at him and I knew it wasn't the rune. So I had some of the guys pull him from the street, Artem spent hours questioning him, so far Artem doesn't sense any lie."

Jace looked at his parabatai, Alec didn't hold any ill regards to Sebastian anymore, but what he did to Max was still a staple in his mind, as well as Isabelle's who was holding Simon's hand. It takes a lot to get Izzy in an emotional state and seeing the man who killed her brother was one of those triggers.

"Alec, Izzy, just watch okay? I don't even trust him 100% but we need to be open-minded." Jace asked, they looked at each other and settled back down, Jace turned back to the monitor

Izzy and Alec didn't say anything else, they just looked tv screen, Jonathan was just sitting on the chair looking at his phone,

"you let him keep his phone?" Clary asked Jace.

"Yeah, who's he going to call? What's he going to say? He got kidnapped by a bunch of half-angelic beings?"

* * *

 

Jonathan was just looking at his phone, Clary enhanced the screen which zoomed in more, she can see he was texting someone, but she couldn't make out who it was or what he was typing. Then his phone rang again, this time a phone call, Jonathan picked it up after the first ring.

_"Yeah,"_

_"Yeah, I'm okay. I told them the truth of course."_ whoever he was talking to knew who they were. Everyone was looking at each other,

" _Why don't you just come here?"_

Jonathan groaned, he was now rubbing his head. _"I know I know, listen in all the years I've known you or remembered you. I think back to that first conversation we had in the crypt where you basically sent me off to my life. You said if I ever needed help I can call you and you'd come. Well, I need your help now."_

"Crypt?" Clary asked Jace, but it was Alec who replied.

"The Crypt in Idris, where the bodies that don't get burnt in the Silent City go and are buried. That's probably where Jonathan became this."

" _No, they left me alone in the interrogation room. Apparently, Clary placed a locking rune that can only be broken by the head of the institute. So I'm stuck here."_

Jon rolled eyes and rubbed his temple again, he was getting annoyed again. Clary needed him to say a name so they could find out who he was talking too, but even alone he was careful with what he said.

" _I don't know. Jace didn't really say how long they'd keep me here."_

_"What do you mean Clave representatives? So you're saying that they are planning to turn me over to the clave? Well that's just bloody brilliant,"_

Shit. Clary forgot about the Clave Representatives that were coming over from Idris tomorrow. Robert and Lydia were among the 4 representatives the Clave would send over. But Clary and Jace haven't met the other two.

"Shit. Jace, he can't be here while the Clave is here."

"Why not? They can deal with him over there." Isabelle said, her voice was laced with anger. Jocelyn turned towards Isabelle and said

"NO. The Clave can't take him he isn't Sebastian. Haven't you been listening?"

"I'm sorry Jocelyn but he is still the man who murdered hundreds of Shadowhunters. Doesn't matter if he's Sebastian or not, he has his face."

"Izzy," Jace said his voice softening,

"No! Jace! I don't care. He killed Max. He killed hundreds of people. He needs to be brought to Justice." Izzy then stormed out of the room, leaving all of them in silence.

"I'll talk to her." Simon and Alec said at the same time.

"I'll go, I'm her brother," said Alec but Simon pulled him back softly,

"Exactly. This issue hits close to home for you too, I'll go."

Simon walked out of the office and went to find Isabelle. Clary turned to Magnus,

"Magnus is what is he talking about possible?"

"I've never heard of it, even years on this earth and Nephilim history and myths is still a mystery to me," Magnus said as he looked at the monitor in front of them, he turned towards Alec, his face was in that neutral mode when he doesn't want people to see his emotions.

Clary was trying to come up with a plan on how they were going to handle this. They couldn't send Jonathan out of the Institute, but he couldn't be here either.

"Jace, what do you think?" She asked, Magnus was right, Jace has been unnaturally quiet through all this. Jace looked around the room, being head of the Institute was a job he never imagined going to him, but it was his, and Clary was in no place to make a proper decision, so he decided to go with his gut choice.

"I think we should keep him here, we can't send him out there. We literally did grab him out of the street and the city is filled with Downworlders who have a vendetta against him, what if one of them were fae and realized who he was? That would be a problem."

"So what are you saying?" Alec asked his parabatai, though knew had a feeling he knew where Jace was getting at and he didn't like it one bit.

"We release him from the interrogation room and put him in a room and hold him there, at least he can get some rest there and we'll figure things out with the Clave tomorrow, I'll send a fire message to Lydia and fill her in as much as I can," Jace said, he left the room before Alec tries to talk him out of this choice.

"Are we actually doing this?" Alec asked, everything was so normal this morning, now they were handling a man who came back from the dead, or someone who was never really dead and has been living an apparent good life and not facing any consequences for what he has done.

They looked back at the man on the screen, he was now just sitting on the chair looking at the mirror in front of him when the door opened.

* * *

Jace came in the room, Jon straighten up and looked at him,

"So am I free to go?" He asked, getting up from the chair, he got 3 more messages from Gen asking him where he was. He was running out of answers.

"Not quite, we can't release you for reasons you don't need to know. But you can leave this room, Clary has opened a room for you to use for the time being until we deal with things,"

"I can't stay here, Jace I have to go back to the hotel. My girlfriend is already wondering where I am."

"This is the best we can do for you. Take it or leave it." Jace was about to leave the room when Jonathan groaned,

Jon knew he wouldn't be able to say or do anything without consequence so he just went with it, at least he was leaving the makeshift cell he's been in for hours.

"Fine. I'll take it but tell me what I want to know." Jace turned his head,

"We'll tell you when we can." Jace motioned for Jon to follow him, the institute was crawling with Shadowhunters, but Jace decided they would take the kitchen stairs, they passed some Shadowhunters and Jon got some stares but what was he expecting? A parade? The hallways were covered in paintings of the Nephilim's throughout the years, then portraits of the Lightwood family with Jace, then of the younger ones.

They stopped in front of a room across one of the training rooms, Jon wanted to do nothing more than train in that room but he has a feeling that he was still technically under arrest so he just followed Jace into the room. The room was simple, with a dark oak double bed in the center of the room, there was a big church window behind it that let in some of the city light, on one side there was the door to watch Jon suspected was a bathroom, and a couch and a table. The other side of the room had a dresser and a wardrobe. On the bed, there were some towels and clothes,

"Just spare clothes, Clary thought you might like to take a shower," Jace excused himself and left Jonathan alone, Jon dropped his jacket on the bed and put his phone on the side table, thank the angel Jon had his backpack with him, he had his computer and his phone charger in there, so he wasn't completely detached from the outside world, he plugged his phone in and headed for the bathroom, Clary was right, he did want a shower, he didn't waste any time he hopped into the shower and relaxed under the water, he wasn't injured but he felt like he was fighting with everything inside him. On the one hand, he was happy they didn't throw him straight in the City of Bones but he was also confused. Jem said he and Tessa would come over in the morning but he wasn't sure if they would actually come. They were in California and though they could easily portal, he understands that Tessa does not like traveling by Portal but it also takes a lot of Tessa's energy because even though he has not seen Jem since the crypt, Jem occasionally checks in on Jonathan via text or calls. And they have become somewhat friends in a couple of years.

After his shower, he put the clothes on, they were just basic sweats, a tank top and joggers he didn't need to reapply the glamor on him since he didn't have to hide his runes to the people in the institute. Once he was settled, or as settled as he could be, he decided to call Gen to tell her that he would not be coming back to the hotel tonight.

" _She insisted I stay the night, it is pretty late and I'm tired so I took the offer. Sorry, I didn't answer earlier we had more issues to work through I guess. I'll see you tomorrow yeah?"_

" _Are you sure everything is okay Jonathan?"_

He hated lying to her, but sometimes lies were needed to protect those people he cared for.

" _Yeah, everything is fine. You should go to bed, we both should. It's already—,"_ he looked at the clock, it was only 9 pm.

_"Huh. I must be more tired than I thought. Listen I'll tell you everything tomorrow okay? I love you."_

_"Love you too."_

They hung up after that Jon didn't know what to do, he was tired but he was a bit wired from the shower and from being in the institute. He was about to on his computer to get some work done, when he heard a knock at the door, he stiffened a bit until he heard his mother's voice. He moved towards the door and opened it, she had a tray of food with her, his stomach growled at the sight he forgot he has not eaten since lunch, he moved to let her in.

"Sorry for bothering you, I was supposed to take some food to you at the interrogation room but Jace told me you were moved. So I brought it here."

She set the food on the table she looked at the bed where his computer was, he saw that she was looking at his laptop.

"Before I was rudely grabbed by whoever grabbed me, I was working on something for my job. It's a publishing party for this book and I'm helping with it because they messed up a few things." He took his computer from the bed and placed it on the table. He was working on edits of another book but he also had the arrangement for the book that was being released soon.

Jocelyn looked at the things Jonathan has done in the past 9 years. She was so upset all his life because his life was taken away from him by Valentine, but now he has lived his life and they dragged him back to this world. Where things are going down and they can't even tell him because it would be dangerous for them and Jonathan.

"This is amazing, I didn't think you would be a writer." Jon looked at her shocked, but he did not show it. Ever since he came back all he wanted to do was to go back to his family and live his life. But he knew it would not be possible. Hearing his mother praise his work made him so happy and proud she gave him a small smile and motioned for him to sit. He sat down next to her, and started to eat the chicken in front of him, Jocelyn ate too,

"It's not my work, I'm just editing someone's work, that's what I do in London, I'm an editor."

They were quiet as Jocelyn read through the manuscript that Jonathan was working on, she read it because she was still trying to come up with something to say to him, what do you say to a son you never really got to know?

"Do you know when Jace and Clary would allow me to leave? Because I do have things to do in New York and I don't think I can come up more excuses." Jon asked after a few moments of silence.

"It's complicated. This has never happened before and with—," Jocelyn didn't finish what she said, but Jon knew what she was going to say.

"With my history of the shadow world, it wouldn't be easy. I try to forget my past but I know I will never forget it. And deep down I don't want to forget what he did. But I made a life with this chance I got. I made a semi-name for myself. A good name and I don't want that to disappear.

"I know. By the look of this, you have something, but you know the rules and the laws of the Shadow World. We'll get more tomorrow, Clary and Jace are dealing with this with a few trusted Clave members and Shadowhunters. 2 of our trusted friends are coming here tomorrow, they just messaged just that they would be portaling in tomorrow. We should know more."

That was probably Jem and Tessa, Jon didn't want to say anything else because he doesn't want them to get in trouble for knowing his whereabouts all this time. So he just kept looking at his mother, nodding.

They talked for a while, Jocelyn asked him about his life in London, how he avoids the Shadow World. She even talked about her life, she has another daughter with Luke, she's called Ava, she showed him a picture of her, she is 7 years old now, she has light dark skin, with hazel eyes, her hair is red but more muted than Clary or Jocelyn's. In the picture she showed him, Ava is sitting on Clary's lap as Clary sketched the birds in front of them Jon smiled at the picture, he showed Jocelyn a picture of him with his friends, last New Years on his phone. It was of him, Gen, Kendra, Nicholas, Jaden, Jasper, Chloe, and Maxium, who is a warlock, Maxium was the only downworlder Jon interacted with, he met Maxium during Holiday in Perth a few years back and they've been stuck with each other ever since. At first, he denied who he was but Maxium didn't seem to care. When Jon asked why he didn't care about his past, Maxium told him that he can sense that he is good in people, that his skin is like a mood ring, it changes color when it senses a person's nature. His skin is naturally gold but when he senses something good in someone, his skin gets this sun-kissed glow.

Jocelyn seemed to notice his warlock friend,

"Yeah he's a warlock, he's probably my best friend because I can be myself with him and not hide you know. I can freely talk about the Shadow World."

Jon noticed the time on the clock, it was nearly midnight, they've been talking for almost 3 hours.

"Wow, it's that late already?" Jocelyn noticed the time too, she wanted to get to know her son more but she knew it was late and they all had an early more tomorrow.

"I'll leave you to it okay? We all have a busy morning tomorrow."

"Are you staying in the Institute?" Jon knew she didn't live in the place with the rest of the Shadowhunters. But he was kind of hoping she would be here in the morning.

"Yeah, it's too late for me to go home, I mean I could always portal, but Clary and I have some things to talk about."

Jocelyn hesitated, but before he could react she took her son into her arms and hugged him tightly, Jon didn't react at first but he hugged her back a few seconds later. He was taller than her but he felt so small in her arms when she first hugged back in the interrogation room his arms were tied up so he couldn't hug her back. But now he could, they let go a few seconds later.

"We'll get through all this okay? Clary just has a lot to think about she's the head of the institute so she has to take a lot of things into mind."

Jocelyn left Jon alone, he didn't know why but he felt lighter since he came here. Like he relaxed a bit knowing he had someone on his side even if it was just his mother. He didn't know how, but he would get them to see him as Jonathan and not Sebastian. He didn't even know how long he would be here because he has his life back in London, but the Shadow World just manage to drag him in. He decided he would deal with this in the morning, for now, he was tired and would go to bed.


	8. Chapter 7:

**Notes for the Chapter:**

> This story is un beta'd so be warned there may be some mistakes. this is in the TMI world but it will be treated as an OC story.
> 
> This is also up on Wattpad my username over there is marielleswriting. That is where I will mainly keep this story up to date.

Jon woke up sweating, his life and past misdoings flash as nightmares in his dream. Only this time he felt bad about what he is doing, he has no demon blood in his system but he can't stop his actions. He killed everyone in his way finally he gets to his family and Gen, Clary and the other shadowhunters try to fight him off, he is yelling inside his head not to do it, he wants to stop but it's like his body doesn't listen. Before he kills his family, or at least that's what it seems, he wakes up, sweating and out of breath. 

He looks at the time on his phone, it was only 4 am but he was still in London time so technically it was 9 am for him. He was already wide awake and couldn't go back to sleep after that dream. He decided to wash off the sweat of his nightmare, then he would finish up the manuscript he was proofreading. Then maybe train a bit, he was in an institute they had 4 training rooms like most institutes do. Thankfully he had one across the room he was in and hopefully it was empty.

Jon quickly showered and change back to the clothes he was wearing yesterday, minus the jacket, he wore the sweatpants again because he did not want to train in jeans. He proofread the manuscript then sent the parts he checked to the publisher aka Gen, she's probably still asleep, so he just added a message in it saying he will be back soon. After finishing the things he had to do for work, like checking his emails and such, also keeping Kendra updated.

Kendra: Hows the big apple? 

Jon: Hectic, working a lot and ran into some family. Tell you later. 

He didn't wait for her reply he just took his phone and his headphones and went to the training room, The sun was still starting to rise so it was still pretty dark, he turned some lights on in part of the room and started with his morning work out. It was nothing extreme, he started with Calisthenics, he's been doing this all his life, it was second nature to him. It was like how Yoga kept some people calm, working out made him calm. He started with push ups, then lunges, followed by sit-ups, then lastly squats. He rested a bit before he did his final set of morning training. Which was done on a punching bag, then some katana training, he hasn't dealt with swords in a while, granted these were basic training swords, they still held the weight of an actual sword. He swung the sword around lunged a bit, feigning at attack.

Jon was focused on his workout that he didn't notice Jace standing by the door. Jace watched him for a while, the way Jonathan moved was so familiar. He should know, he's been on the other end of that sword. But it was also because Valentine trained them the same way all their lives. While Jace's training was intense he knew Jonathan's was different and more difficult. He's seen the scars on Jonathan, he pretended he didn't notice them but he knows they're there. Jon had music playing so he didn't notice Jace. Clary was still asleep in their room so he couldn't do his workout there, this training room was closest to their room so he came here, he didn't expect to see Jonathan.

Jonathan finally notices Jace by the door when he turned his way, he stopped and to catch his breath.

"Sorry I didn't think anyone would be up this early," Jon said putting the Kanata back in its holder since he finished. And grabbed his towel and water bottle, which he probably got in the vending machine Simon had put in, he wanted it to be filmed with junk food, but Jace and Alec said no so they filled it with water, and energy bars, and fruit.

"What are you doing?" Jace asked Jon, who was getting ready to leave the room.

"Going back to my room?" Jon said, slightly confused.

"Why? Were you done with your workout? It's a big room meant for at least 20 shadowhunters to train in."

Jon didn't argue, though honestly he just wanted to leave because of the impending conversation he knew Jace wanted to have.

"Wanna spare? I can't imagine that the mundane world had people capable of sparring with you," said Jace who was stepping onto the mat, Jon looked at Jace a bit surprise, but he didn't argue, he was right, he sparred with others before and they kept up with him but fighting with another Nephilim was different. Besides, he knew Jace's fighting style so this would be quick.

"You think you can keep up?" Jonathan said smiling as he got on the mat, Jace smirked,

"I'm the best shadowhunter of the generation, don't worry about me." They got into a fighting stance, they circled each other for a few seconds, watching what the other would do. They were both thinking how the other fights, they've seen each other fight before, but this was training and they weren't trying to hurt each other, at least Jon wasn't. He wouldn't blame Jace for wanting to hurt him. After a few moments of doing nothing, Jonathan made the first move

(I cannot write fighting/training to save my life so picture it as you will)

They were both out of breath by the end of it. Jace had Jonathan pinned under his foot, Jace let his guard down so Jonathan tripped him and got up from the floor. He helped Jace up,

"Okay, so I guess the mundane world didn't make you soft." Jace took Jonathan's hand and got up. He looked at the clock on the wall and it was already 6 am. Clary should be awake by now, Jem and Tessa said they would arrive by 7, a few hours before the Clave arrives.

"Our friends are arriving soon, they're coming from L.A. Clary wants you to meet them so meet us in the library. You remember where it is?" Jace asked Jon nodded, he's been there once before, back when Jace was bonded to him they went there to get a book he needed. Jace didn't say anything else before leaving. Jon went back to his room and just showered again, He hated the feeling of sweat, he didn't really have any other clothes so he just but his button up shirt back on and his jeans then headed for the library, he was on the second floor and if he remembered correctly the library was on the 3rd. He took the lift, he thought fewer chances of running into other Shadowhunters. Spoke too soon, as soon as he entered the lift he saw Alec Lightwood, and man if looks could kill the look Alec gave him would have had him from the moment he stepped into the lift. He was surprised that Alec didn't do anything but glare at him, the ride was quick but it was the longest elevator ride he's ever experienced. They both  stepped out of the lift. It looks like Alec was coming to the meeting, great, he'll experience more of his glaring.

When they both entered the room all eyes were on them, Clary's was on Jon, then on Alec. Jace kept his eye on his Parabatai, Jace looked over the two of them, they both seemed to be in one piece. Jon looked around and saw that it was just his mother, Clary, Jace, and Alec. Alec's sister or Clary's parabatai were nowhere in sight. But he did see Jem and Tessa, who were both sat on the sofa. Jem gave him a slight nod, that you wouldn't even notice if you weren't looking at him.

"Jon, these are our friends. James Carstairs, and Tessa Gray."

Jem looked at as if he was asking, can we tell them, Jon shrugged, might as well.

"Oh Jonathan I told you to stay away from New York." and as expected everyone's eyes went on them.

"I didn't expect to be grabbed, I had glamour runes placed on me to keep me protected from anyone who is part of the shadow world. Show's how strong runes are." He said, he looked at Tessa and gave her a small smile, Tessa got up and quickly moved towards him and hugged him, unlike Jem, Jon has seen Tessa face to face plenty of times before. She would have business in London and would check up on him often to see how he was adjusting to the mundane world, and once he was well adjusted they would just take about little things, always avoiding the topic of his family and what has happened in his old life. She looked so young like most warlocks do, but she had such an old soul, her eyes have seen way worse than him and she didn't look at him with distrust, more like curiosity.

"what the hell is going on?" Alec asked he didn't like how their friends seemed to know Jonathan, Clary insisted they call him Jonathan and not Sebastian, no matter what name he had, Alec still didn't trust him,

"Jon is a friend of ours" Tessa said "and I know his past has a lot of fire but I can vouch for him with the clave of how much he has changed, and so can Jem. We've kept an eye on him and he has made a life for himself, even with struggles here and there, that we wouldn't share, he is doing fairly well. So I suggest you tell him the real reason you are keeping him here. It's important that he knows for his sake and yours." Tessa said she was always straight to the point, for years Tessa says she tries to separate herself from Nephilim business but she was half Nephilim she could never really separate herself. So now she just accepts it.

It was Jon's turn to be confused, he looked at Clary and Jace,

"What is she talking about? What's going on?"

"Has the mundane world dulled your senses?" Another warlock entered the room, Magnus Bane, "Tell me you can't feel that pulse of demonic energy like it's drawing you in? You may not have demon blood anymore Jonathan, but you can't get rid of that feeling you feel. Tessa and I feel it every single minute."

Jon wants to say he didn't know what Magnus was talking about, but that would be a lie. For months now he has felt it. Maxium told him that it was the reason for his nightmares. This looming darkness that has shadowed those with demonic blood. The warlocks can hide that feeling but it gets a hold on them every once in a while. Maxium went to the Spiral Labyrinth to learn more about it and he hasn't been back since, he sends Jon messages here and there, but he has been silent for a while. He meant to ask Tessa about Maxium but they were kind of caught up at the moment.

"So you can feel it. What do you think it is?" Magnus asks, coming closer to him that he was now in front of him. Looking him straight in his eyes, green on gold.

"I don't know." He said, and he was telling the truth, he knows something is happening but he has been away from the Shadow World for a long time now, he didn't know what was going on between the Downworld.

Clary took pity on her brother, she was looking at his hands and his nails were causing him to bleed.

"Jonathan," Clary said, her tone serious. Jon tore his gaze from Magnus and released his grip on his palms, he looked down at the marks his nails made on is palm, he was bleeding.

"It's the Seelie Queen, Jon. After the Cold Peace and the War." Jon looked away when Clary mentioned the war that he started.

"We signed a treaty that made sure the faeries who participated in the war were to pay for what has happened. Since you were "dead" the punishment went to them. The Seelie Queen then appeared a few months ago with the news."

"Well you might as well sit down, this is going to take a while to explain."


	9. Chapter 8:

**Notes for the Chapter:**

> This story is un beta'd so be warned there may be some mistakes. this is in the TMI world but it will be treated as an OC story.
> 
> This is also up on Wattpad my username over there is marielleswriting. That is where I will mainly keep this story up to date.

Clary went into details of what has happened to the shadow world in the last few years. She explained to him how the Shadow World was rebuilding after the war, every time they mention the war, Jonathan always gets a far away look in his eyes, but this time it disappeared faster than it normally did. Clary went to explain what the Cold Peace was, how it was to punish the faeries for their participation in the war.

"Why punish them all? It was only the Seelie Queen's Court who assisted."

"You know how the clave are Jonathan, what a big war does to them." she sighed,

"They—we" Clary corrected herself, because at the time it did make sense to them, even though they didn't agree with what it did to the Shadowhunters with faerie blood in them, like Mark and Helen Blackthorn, and Artem, it was the best thing to do.

"We thought it would be for the best, even though some of the Nephilim with faerie blood had to suffer," Clary said playing with the ring on her finger, at first glanced it looked like a wedding ring, but it was only her Fairchild Family Ring. Jonathan looked at her neck and saw the Morgenstern ring around it, his was around his neck too, but it was tucked in under his shirt.

"A few years ago, there was an issue that happened in Los Angeles, I don't want to go into detail because it isn't my story to tell, but a lot of things happened and that was when the faeries emerged. They were quiet for years but that sparked everything for them. The Seelie Queen appeared outside of her court for the first time in millenniums, but she wasn't alone."

Clary stopped and looked at everyone in the room, Jon did the same, though no one would meet his eyes, not even Tessa and Jem. Clary cleared her throat, and looked back towards her brother, she hesitated for a moment then walked up towards where he sat and sat across him, on the coffee table. Jace followed her as well, Alec was still stood by the wall, although he stopped leaning on the surface and just crossed his arms.

"What?" Jonathan asked he hated not knowing what was happening that was the one thing that didn't change in him.

"She had a child with her," Clary said, looking at her brother's eyes, but he didn't seem to be putting the pieces together. She herself didn't believe what the queen had said when she first came out of her court, that the young Nephilim child with her, who was 4 at the time, was Jonathan's child. But then the queen put him in front of her and there was no denying that he was her brother's son, he looked like the way Jonathan had looked when he was still Sebastian but the child's features were much softer, he had heterochromia, one eye was black and the other green, like the eyes that Jonathan now has, to the red hair, that perfectly matched the queens scarlet locks. The only indication that the child was somewhat Fae was his ears and his green eye, that seemed to be the color of the trees, moss, and everything that embodied nature rolled into one.

"Jonathan, this child was Nephilim," Clary said,

Jonathan was shocked at the news at first, then it dawned on him. That last couple of months of that life, the Seelie queen, Iris, (the name she used with Jonathan, she had so many names she didn't care which she used her subjects called her your majesty or my queen) and he were growing somewhat close. She was the only one who did not question his actions, she was a challenge for him, they spent the night together but he never realized that she became pregnant.

"Jonathan she's becoming a big problem for the Down World and for us. She's threatening to start a war for what happened with the cold peace. She cannot be reasoned with." Jocelyn said she was now standing in front of Clary and Jon.

"Is that why you kept me here? Because of here?"

"That's one reason. The other is we still don't know what to do with you," said Jace his arms crossed in front of him.

Jonathan sighed and rubbed his head. Everything was getting out of control, he should have just said no to New York. But there was a voice in his head that said that he had to be here. He had to do something about the queen, and his son. Jonathan's breath hitched.

"What is it? Jocelyn asked,

"I have a son." He said gently, not looking anyone in the eyes, he had a faint smile on his face.

Jocelyn gave him a small smile, "yeah you do."

"That's not a good thing," Alec said, Jon forgot he was in the room he was so quiet he thought that he had left.

"That child is a mixed of Sebastian and the queen, who knows what evil he will bring."

Clary has never seen someone react so quickly, Jonathan was up and walked towards Alec with a speed she has never seen. If Jace weren't standing so close to Alec, Jon might have done something he would regret later.

"He is only a child," his voice sounding eerily like Sebastian when he is angry. Alec jumped a bit but regain his composure. He moved his face towards Jon's.

"Yes, but he is your child. And I don't trust you." Alec sneered at Jonathan

"Alec" Jace warned, his grip on Alec's arm tightening a bit he did not want his parabatai to do something he would regret. Alec looked at Jace then at Magnus who moved closer to him. Alec broke himself free of Jace's grip and left the room, Magnus was about to follow him when Jace out a hand on Magnus's shoulder. "Let him cool down for a minute."

Jem and Tessa looked at each other, "Jonathan, you have to be careful. If the Seelie Queen realizes you are here and not the way that you were who know's what she will do. You a safer here than out there, at least until we find out what to do." Tessa said.

"I cannot stay in the Institute, you are having Clave representatives over and once they realize that I am here, well I would rather take my chances with the Queen."

"This for our safety as well Jonathan. We get to keep an eye on you and the Seelie Queen won't know you are back."

"I HAVE A LIFE JACE!" he said loudly,

"A life that I build. That I finally got, a girlfriend who is wondering where I disappeared too, a job that I have to do, a home in London."

Tessa understood. London was a beautiful place that she always manages to find herself in when she needed to feel closer to her family. She had wonderful memories there. She and Jem, when they were ready, were going to raise a family there. She understood Jonathan's want to be back in the city that gave him a second chance at life.

"Jonathan this won't be forever. Tell Genevieve what you can but you can't go back."

The look Jonathan gave her made her heart ache, she had grown fond of the man in front of her. She did the job of visiting him because London was still a fresh wound for Jem, she did not blame him. So Tessa understood Jonathan a bit more, she watched him build his life, and it was a good one too. She lived as a mundane before and it was a content life for her because it was all she knew, but Jonathan had to learn it all and he was a quick learner.

"If you go back your girlfriend would be in danger, you friends. The Queen is relentless in what she wants and if she knows you are back who knows what she will do. She might already know you are alive. I mean she has spies in the cities, at least here you are safe and so is your girlfriend. I agree with Tessa, you have to tell her to leave the city."

Jonathan knew he didn't really have much of a choice. He had to stay or Gen and his friends would be in danger.

"I have to tell her in person. I can't do it over the phone."

Clary sighed, "Jonathan you can't—," Jon interrupted her,

"You are taking away my life you can at least let me say goodbye to her in person."

"It's not forever," Clary said, she understood why he was angry, no rune power would calm this.

"I'll go with him," Jocelyn said, "I'll go with him to his hotel, we'll portal there and we will be in and out quickly and be back."

Clary and Jace looked at each other, they knew it was a risk but it would get Jonathan away from the council while they find a way to explain to them what he doing alive. Also, it would give him time to take in all the things they had told him.

"Take Theo and Amber with you, they can be extra protection if you need it."

Jonathan took the chance, he left the library and headed back down to his room. He didn't bring his bag since it seemed that he would be here for a while. He just took his phone and sent Gen a quick text that he was coming back. Once outside his room, his mother and two other Shadowhunters were waiting for him. Clary and Jace must have told the institute about him already because they did not seem shocked to see him. They were guarded but fewer weapons heavy that he thought, they had daggers with them and a seraph blade but that was about it. He nodded to his mother and she drew the portal. He told her the hotel he was staying in last night so he didn't have to tell her again, Theo stepped into the portal first followed by Jonathan and Jocelyn, Amber came out last. They were on the side of the hotel in a small park area that connects with the hotel.

"You two are glamoured, right? My mother I cam explain, but I can't explain two people with weapons dressed in all black."

The two of them looked at each other and activated their glamor rune. Jonathan took a deep breath he activated his rune too, he was only wearing his t-shirt so his runes on his arms were visible he did not want Gen to see them, she's been around him so long that she was starting to see through the illusion. She couldn't see the Shadow World but she's managed to see a rune or two once before. They headed into the hotel lobby towards the elevator. Gen texted him back that she just got back from the meeting with the publishing house, she explained why he could make it.

There is no going back after they enter the elevator.


End file.
